Closed kfuku52 closed 1 year ago
SRA for ERR1752086 is empty in the database. amalgkit now handles it correctly.
/Users/kf/miniconda3/bin/python /Users/kf/Dropbox/repos/amalgkit/amalgkit/amalgkit getfastq --out_dir . --threads 4 --remove_sra no --remove_tmp no --id ERR1752086 --aws yes --gcp yes --ncbi yes --redo yes
AMALGKIT version: 0.6.8.0
AMALGKIT command: /Users/kf/Dropbox/repos/amalgkit/amalgkit/amalgkit getfastq --out_dir . --threads 4 --remove_sra no --remove_tmp no --id ERR1752086 --aws yes --gcp yes --ncbi yes --redo yes
AMALGKIT bug report: https://github.com/kfuku52/amalgkit/issues
amalgkit getfastq: start
pigz found. It will be used for compression/decompression in read name formatting.
--id is specified. Downloading SRA metadata from Entrez.
Entrez search term: ERR1752086
Number of SRA records: 1
processing SRA records: 0 - 1
Filtering SRA entry with --layout: auto
Individual SRA size of ERR1752086: 999,999,999,999 bp
Number of SRAs to be processed: 1
Total target size (--max_bp): 999,999,999,999,999 bp
The sum of SRA sizes: 999,999,999,999 bp
Target size per SRA: 999,999,999,999,999 bp
Processing SRA ID: ERR1752086
spot_length cannot be obtained directly from the metadata.
Using total_bases/total_spots instead: 1
Library layout: single
Number of reads: 999,999,999,999
Single/Paired read length: 1 bp
Total bases: 999,999,999,999 bp
Processing ERR1752086 as publicly available data from SRA.
Previously-downloaded sra file was not detected. New sra file will be downloaded.
No source URL is available. Check whether --aws, --gcp, and --ncbi are properly set.
Trying to download the SRA file using prefetch.
Command: prefetch --force no --max-size 100G --output-directory ./ ERR1752086
Empty value(s) of total_bases were detected in ERR1752086. Filling a placeholder value 999,999,999,999
Empty value(s) of total_spots were detected in ERR1752086. Filling a placeholder value 999,999,999,999
/Users/kf/Dropbox/repos/amalgkit/amalgkit/getfastq.py:798: FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)`
metadata.df.loc[is_total_spots_na, 'total_spots'] = new_values
AWS_Link is empty and will be skipped.
GCP_Link is empty and will be skipped.
NCBI_Link is empty and will be skipped.
Exhausted all sources of download.
prefetch did not finish safely. Trying prefetch again.
prefetch stdout:
prefetch stderr:
2022-12-11T09:15:08 prefetch.2.10.0 err: name not found while resolving query within virtual file system module - failed to resolve accession 'ERR1752086' - no data ( 404 )
Again, prefetch did not finish safely.
Traceback (most recent call last):
File "/Users/kf/Dropbox/repos/amalgkit/amalgkit/amalgkit", line 383, in <module>
args.handler(args)
File "/Users/kf/Dropbox/repos/amalgkit/amalgkit/amalgkit", line 37, in command_getfastq
getfastq_main(args)
File "/Users/kf/Dropbox/repos/amalgkit/amalgkit/getfastq.py", line 850, in getfastq_main
download_sra(metadata, sra_stat, args, sra_stat['output_dir'], overwrite=False)
File "/Users/kf/Dropbox/repos/amalgkit/amalgkit/getfastq.py", line 301, in download_sra
assert os.path.exists(path_downloaded_sra), 'SRA file download failed: ' + sra_stat['sra_id']
AssertionError: SRA file download failed: ERR1752086
prefetch stdout:
prefetch stderr:
2022-12-11T09:15:09 prefetch.2.10.0 err: name not found while resolving query within virtual file system module - failed to resolve accession 'ERR1752086' - no data ( 404 )
Process finished with exit code 1